lissero 0.4.0

MDU Listeria Serotyping

LisSero

In silico serogroup and binary typing prediction for Listeria monocytogenes

Authors

• Jason Kwong (@kwongjc) - GitHub: kwongj
• Torsten Seemann (@torstenseemann) - GitHub: tseemann

Maintainers

• MDU PHL - Josh Zhang, Kristy Horan, and Anders Gonçalves da Silva

Dependencies

• Python 3.6+
• BLAST 2.10.0

Installation

pip3 install lissero

Installing BLAST 2.10.0

Brew:

brew install blast

Conda:

conda install -c bioconda blast 

In silico serogrouping for Listeria monocytogenes

LisSero is based on a method of predicting serogroup for Listeria monocytogenes using PCR, as described by Doumith et al (see References). It detects the presence or absence of 5 DNA regions (lmo1118, lmo0737, ORF2110, ORF2819 and Prs). The patterns obtained reflect the four main serotypes (1/2a, 1/2b, 1/2c, and 4b) obtained from food and human sources.

The patterns are not based on genes involved in somatic (O) or flagellar (H) biosynthesis, and are not specific to just one serotype, but rather to a group of serotypes.

Serogroup	lmo1118	lmo0737	ORF2110	ORF2819	Prs
1/2a, 3a	-	+	-	-	+
1/2b, 3b, 7	-	-	-	+	+
1/2c, 3c	+	+	-	-	+
4b, 4d, 4e	-	-	+	+	+
4b, 4d, 4e*	-	+	+	+	+
Listeria spp.					+

If only Prs is detected, these isolates are often serotype 4a or 4c, though LisSero reports these as "Nontypable".

Usage

$ lissero --help

Usage: lissero [OPTIONS] FASTA...

  In silico serogroup prediction for L. monocytogenes. Alleles: lmo1118,
  lmo0737, ORF2819, ORF2110, Prs

  References:

  * Doumith et al. Differentiation of the major Listeria monocytogenes
  serovars by multiplex PCR. J Clin Microbiol, 2004; 42:8; 3819-22

Options:
  -s, --serotype_db TEXT
  --min_id FLOAT          Minimum percent identity to accept a match. [0-100]
                          [default: 95.0]

  --min_cov FLOAT         Minimum coverage of the gene to accept a match.
                          [0-100]  [default: 95.0]

  --debug
  --help    

Bugs

Please submit via the GitHub issues page: https://github.com/MDU-PHL/LisSero/issues

Software Licence

GPLv2: https://github.com/MDU-PHL/LisSero/blob/master/LICENSE

References

• Doumith et al. Differentiation of the major Listeria monocytogenes serovars by multiplex PCR. J Clin Microbiol, 2004; 42:8; 3819-22.